Module 1 - Early Earth and the diversification of life

Module 1: Early Earth and the Diversification of Life Origin of earth Origin of life  models for how life might have started  RNA world  Metabolic Diversification: Consequences for Earth’s Biosphere  Photosynthesis and the Oxidation of the Earth  The Rise of Oxygen: Banded Iron Formations  Origin of eukaryotic cells and the endosymbiotic theory Brief History of Life on Earth The Tree of Life oldest known sedimentary rocks date to 3.86 billion years ago, indicating that oceans were present at the time these rocks were formed. These rocks contain fossilized remains of what appear to be cells (see figure on right), and carbon with isotopic ratios that provide further evidence for ancient microbial life. Oldest facts!  oldest known Earth minerals (date to 4.4 billion years ago, or 4.4 bya)  oldest known rocks on Earth (4.1 bya)  oldest known meteorites (4.6 bya; for the age of the solar system) Origin of Earth The Blue Marble, the most widely used photograph of Earth, taken by the Apollo 17 mission in 1972. Earth formed ~4.5BYA based on analysis of slowly decaying radioisotopes. It was formed as a result of nuclear fusions on the sun (formed from supernova event). Earth cooled over time, a metallic core, rocky mantle, and a lower-density, thin surface crust formed. Early Earth was inhospitable, characterized by a molten surface under intense bombardment by asteroids and other objects from space, which was thought to have persisted for over 500 million years. The intense heat and the absence of liquid water indicate that early Earth was certainly a “sterile planet. “ Analyses of ancient zircon crystals indicate the presence of solid crust and liquid water on the earth as early as 4.3 billion years ago Further evidence based on carbon isotope ratios of graphite materials in zircon minerals suggest biogenic origin, providing evidence for life on Earth 4.1 billion years ago. Scanning electron micrograph of microfossil bacteria from 3.45-billion-year-old rocks of the Barberton Greenstone Belt, South Africa. Note the rod-shaped bacteria (arrow) attached to particles of mineral matter. The cells are about 0.7 μm in diameter. – Madigan et al. 2019, Brock Biology of Microorganisms Origin of Life If life developed from non-living matter then 4 requirements need to be fulfilled on the conditions of the early earth: 1. little or no free oxygen: oxygen breaks bonds (oxidizes so O2 is not conducive to building molecules) (oxidizes = breaking apart) Where did the oxygen we have today come from? 2. abundant energy source: to build biological molecules. Energy could have been derived from violent thunderstorms, volcanic activity, meteorite bombardment, intense radiation (lots of UV; no ozone layer) 3. occurrence of chemical building blocks, dissolved inorganic minerals . The atmosphere contained gases such as CO 2, H2O vapor, CO, H2 and N2 in early earth can be found on meteorite (and small amounts of NH3, H2S, and CH4 (no O2) 4. time: for molecules to react with one another .Estimated earth is 4.6 billion years old .Evidence that life arose on earth ~ 3.5 bya. So, it took 1.1 billion years for life to take form? Attempts to reconstruct the early Earth’s atmosphere and chemical profile have led to production of organic molecules from simpler materials, in the presence of some form of energy 1 In the 1920s , Oparin and Haldane independently proposed that organic molecules could form spontaneously from simpler raw materials when sufficient energy is supplied in a reducing (energy-rich, electron-adding) environment 2 In the 1950s , Miller and Urey created a “reducing atmosphere” of H2O, H2, NH3, CH4 in a spark chamber; after sparking, they found that amino acids and other organic compounds had formed    designed to mimic what was thought at the time to have been Earth’s early atmosphere later experiments with different “reducing atmospheres” that were thought to be better matches to the likely atmosphere of the early. Earth produced all 20 amino acids used in proteins, various sugars and lipids, and components of DNA and RNA nucleotides current models of the Earth’s early atmosphere are that in general the atmosphere was not reducing, but that there were likely many local environments that were reducing – especially near volcanic activity 3. organic polymers can form spontaneously from monomer building blocks on some sand, clay, or rock surfaces Models for how and where life started:  prebiotic broth hypothesis – life began from an “organic soup” in the oceans  bubble hypothesis – a variation on the prebiotic broth, with “oily bubbles” from an organic soup interacting with land surfaces at shallow seas or seashores  iron-sulfur world hypothesis – life began from an “organic soup” interacting with mineral surfaces at hydrothermal vents in the ocean floor, with abundant iron and sulfur there impacting the early metabolism that developed  deep-hot biosphere hypothesis – life began in an “organic soup” deep within the Earth  exogenesis – earth was seeded with life from an extraterrestrial source  religious/Christian belief – life was created by a Divine Creator Submarine mounds and their possible link to the origin of life. Model of the interior of a hydrothermal mound with hypothesized transitions from prebiotic chemistry to cellular life depicted. Inset: photo of an actual hydrothermal mound. Hot, mineral-rich hydrothermal fluid mixes with cooler, more oxidized ocean water, forming precipitates of Fe and S compounds, clays, silicates, and carbonates. Mineral precipitates form pores that could have served as energy-rich compartments that facilitated the evolution of precellular forms of life. – Fig 13.3 of Madigan et al. 2019, Brock Biology A model for how the first cells could have originated and functioned A. Protobionts that resemble living cells , the evolutionary precursor of prokaryotic cells 1. microspheres, a type of protobiont, that form spontaneously when liquid water is added to abiotically produced polypeptides 2. microspheres can grow, divide, and maintain internal chemistry different from their surroundings 3. microspheres show that some spontaneous production and maintenance of organization is possible, but are incomplete as a model for formation of the first cells B. genetic reproduction was crucial in the origin of true cells 1. RNA likely was first (RNA world hypothesis) -RNA can catalyze a variety of reactions, including some selfcatalytic reactions -RNA can also store genetic information -in vitro evolution of RNA has shown that the RNA world hypothesis is feasible – selection can act on self-replicating RNA molecules in vitro 2. DNA likely came later and had the selective advantage of greater stability a possible energy-conserving scheme for primitive cells. Formation of pyrite (FeS2) leads to H2 production and So reduction, which fuels a primitive ATPase. Note how H2S plays only a catalytic role; the net substrates would be FeS and So . Also note how few different proteins would be required. G0′ = -42kJ for the reaction FeS + H2S → FeS2 + H2. About RNA:  RNA is a component of certain essential cofactors and molecules found in all cells (such as ATP, NADH, and coenzyme A)  RNA can bind small molecules (such as ATP, other nucleotides, and amino acids);  it can possess catalytic activity;  it is known to catalyze protein synthesis through the activities of rRNA, tRNA, and mRNA  possible to imagine that certain RNA molecules once had the ability to catalyze their own synthesis; these earliest forms of life may have had little or no need for DNA or protein Alternative source of H2 Proton motive force drives energy conservation A. the first evidence of life in the fossil record are isotopic carbon “fingerprints” in rocks from ~3.8 bya B. the first evidence of cells are microfossils of prokaryotic cells in fossils of stromatolites dated to ~3.5 bya 1. stromatolites are rocklike structures made up of layers of bacteria and sediment 2. in some areas stromatolites are still being formed today The earliest self-replicating biological systems may have been based on catalytic RNA. At some point RNA enzymes evolved the capability to synthesize proteins, and proteins became the main catalytic molecules. Conversion from RNA- to DNA-based genomes required the evolution of DNA and RNA polymerases. The lipid bilayer is the site of electron transport and the evolution of this structure was likely important for energy conservation, in addition to containing and protecting biomolecules. The last universal common ancestor (LUCA), which preceded the divergence of Bacteria and Archaea (see Figure 13.9), was a cellular organism that had a lipid bilayer and used DNA, RNA, and protein. Horizontal gene transfer (HGT) may have allowed rapid transfer of beneficial genes among early forms of life. C. the first cells were most likely anaerobic heterotrophs 1. there was likely an abundance of organic molecules available for food early on 2. later, as organic molecules became scarcer, photosynthetic organisms were favored D. the first photosynthetic organisms were likely the purple and green sulfur bacteria, which use H2S as a hydrogen donor Metabolic Biosphere   “The earliest cellular forms of life likely possessed elements of this three-part system of DNA, RNA, and protein, in addition to a membrane system capable of conserving energy.” Diversification: Consequences for Earth’s The energy-generating metabolism of primitive cells would have been exclusively anaerobic. During this era CO2 may have been the major source of carbon for cells (autotrophy)  because abiotic sources of organic carbon would quickly have become limiting as life became more and more abundant on Earth.  abiotic sources of fixed nitrogen would have become limiting on the early earth, and microbes evolved the ability to use atmospheric N2 as a source of nitrogen (nitrogen fixation) as early as 3.2 billion years ago, as indicated by isotopic ratios of nitrogen found in ancient sedimentary rocks.    the first evidence of cells are microfossils of prokaryotic cells in fossils of stromatolites dated to ~3.5 bya 1. stromatolites are rocklike structures made up of layers of bacteria and sediment 2. in some areas stromatolites are still being formed today the first cells were most likely anaerobic heterotrophs (a heavy sounding term for non-photosynthetic cells/organisms that do not use oxygen as terminal electron acceptor in respiration) 1. there was likely an abundance of organic molecules available for food early on 2. later, as organic molecules became scarcer, photosynthetic organisms were favored   the first photosynthetic organisms were likely the purple and green sulfur bacteria, using electron donors such as H2S for CO2 fixation and generating elemental sulfur (S0) as a waste product It is widely thought that H 2 was a major fuel for energy metabolism of early cells. This hypothesis is also supported by the Tree of Life, in that virtually all of the earliest branching organisms in the Bacteria and Archaea use H2 as an electron donor in energy metabolism and are also autotrophs. Elemental sulfur (S0) may have been one of the earliest electron acceptors, as the reduction of S 0 to yield H2S is exergonic and would likely have required relatively few enzymes (review figure on slide 15) Because of the abundance of H2 and sulfur compounds on early earth, this scheme would have provided cells with a nearly limitless supply of energy. Other early microorganisms may have used H2 and CO2 to produce acetate or methane. Such metabolism is called chemolithotrophic metabolism driven by H2 and would likely have supported the production of large amounts of organic compounds from autotrophic CO2 fixation. Over time, these organic materials would have accumulated and could have provided the conditions needed for the evolution of new chemoorganotrophic bacteria with diverse metabolic strategies to conserve energy from the oxidation of organic compounds. First life, however, it came to be:  the first evidence of life in the fossil record are isotopic carbon “fingerprints” in rocks from ~3.8 bya -Fig. 13.6 of Madigan et al. 2019, Brock Biology of Microorganisms FACT: Stromatolites, or “layered rocks,” are formed when certain kinds of microbial mats cause the deposition of carbonate or silicate minerals that promote fossilization Ancient and modern stromatolites A. The oldest known stromatolite, found in a rock about 3.5 billion years old from the Warrawoona Group in Western Australia. Shown is a vertical section through the laminated structure preserved in the rock. Arrows point to the laminated layers. B. Stromatolites of conical shape from 1.6-billion-year-old dolomite rock from northern Australia. C. Modern stromatolites, Darby Island, Bahamas. The large stromatolite in the foreground is about 1 m in diameter. (d) Modern stromatolites composed of thermophilic cyanobacteria growing in a thermal pool in Yellowstone National Park, USA. Each structure is about 2 cm high. (e) Modern stromatolites from Shark Bay, Australia. Individual structures are 0.5–1 m in diameter. A. One-billion-year-old microfossils from central Australia that resemble modern filamentous cyanobacteria. Cell diameters, 5– 7 μm. B. Microfossils of eukaryotic cells from the same rock formation. The cellular structure is similar to that of certain modern green algae, such as Chlorella species. Cell diameter, about 15 μm. Color was added to make cell form more apparent. The Rise of Oxygen: Banded Iron Formations Stromatolites are largely gone from Earth today, but modern examples of this ancient microbial ecosystem can still be found in certain shallow marine basins or in hot springs Photosynthesis and the Oxidation of the Earth  The ability to use solar radiation as an energy source allowed phototrophs to diversify extensively.  By 2.5–3.3 bya, the cyanobacterial lineage evolved a photosystem capable of oxygenic photosynthesis in which H2O supplanted H2S as the reductant for CO2, thereby generating O2 as a waste product.  The origin of oxygenic photosynthesis and the rise of O 2 in Earth’s atmosphere caused the greatest change ever in the history of our biosphere and set the stage for the evolution of even newer forms of life that evolved to exploit the energy available from O2 respiration.  Cyanobacteria were likely the first photosynthetic organisms  stromatolites from as old as 3.5 bya containing what appear to be fossil cyanobacteria  many stromatolites with what appear to be fossil cyanobacteria date to about 2.5 BYA Banded iron formations. An exposed cliff made of sedimentary rock about 10 m in height in Western Australia contains layers of iron oxides (arrows) interspersed with layers containing iron silicates and other silica materials. The iron oxides contain iron in the ferric (Fe3+) form produced from ferrous iron (Fe2+) primarily by the oxygen released by cyanobacterial photosynthesis. – Fig. 13.8 of Madigan et al. 2019, Brock Biology of Microorganisms  In the absence of O2, most of Earth’s iron would have been present in reduced forms (Fe0 and Fe2+) and large amounts of iron would have been dissolved in Earth’s anoxic oceans. Molecular and chemical evidence indicates that oxygenic photosynthesis first appeared on Earth several hundred million years before significant levels of O 2 appeared  BUT the O2 that cyanobacteria produced could not accumulate in the atmosphere because it reacted spontaneously with the reduced iron minerals in the oceans to make iron oxides. By 2.4 bya, O 2 levels had risen to one part per million, a tiny amount by present-day standards, but enough to initiate what has come to be called the Great Oxidation Event (see figure in slide 27)  The metabolism of cyanobacteria yielded O 2 that oxidized reduced minerals containing Fe2+ to iron oxides containing Fe3+. This led to banded iron formations, -Fig. 13.7 of Madigan et al. 2019, Brock Biology of Microorganisms Ancient stromatolites contain microfossils that appear remarkably similar to modern species of phototrophic bacteria    laminated sedimentary rocks formed in deposits of ironand silica-rich materials and an indication of the release of O2 into the oceans As O2 accumulated on Earth, the atmosphere gradually changed from anoxic to oxic (see figure in slide 27). Species of Bacteria and Archaea unable to adapt to this change were increasingly restricted to anoxic habitats because of the toxicity of O2 and because it chemically oxidized the reduced substances upon which their metabolisms depend. Other schemes of metabolism came about such as sulfide oxidation, nitrification, and the various other aerobic chemolithotrophic processes (more in MCB101) . Microbes that evolved the capacity to respire O2 gained a tremendous energetic advantage because of the high reduction potential of the O2/H2O couple (aerobic respiration), and with more energy at their disposal, aerobes could reproduce far more rapidly than anaerobes. The formation of the ozone layer (O 3) soon after oxygenation of the atmosphere provided protection from UV radiation and allowed life to expand to regions at and near the Earth’s surface . Prior to the generation of the ozone shield, the punishing UV irradiation from the sun would have made Earth’s surface fairly inhospitable for life, restricting life to environments that provided protection. Bigger Picture Major landmarks in biological evolution, Earth´s changing geochemistry, and microbial metabolic diversification The oldest date for the origin of life is fixed by the time of Earth’s origin, and the minimum time for the origin of oxygenic photosynthesis is fixed by the Great Oxidation Event, about 2.4 billion years ago (BYA). Note how the oxygenation of the atmosphere from cyanobacterial metabolism was a gradual process, occurring over a period of about 2 billion years. Eukaryotic cells descended from prokaryotic cells  Eukaryotes first appear in the fossil record about 2BYA, long after prokaryotic cells  DNA sequencing provides evidence of common ancestry of life on Earth, with eukaryotes splitting from Archaea about 2 BYA (see figure of the Tree of Life on slide 19)  Recall the endosymbiotic theory – model for how at least some of the eukaryotic cell organelles came to exist , e.g. the mitochondrion of modern-day eukaryotes arose from the stable incorporation of a bacterium capable of aerobic respiration into the cytoplasm of early eukaryotic cells. “Evolutionary origins of microorganisms remained a mystery until it was discovered that certain molecular sequences are a record of evolutionary history. Mutations occur at random and accumulate over time, causing heritable changes in the sequence of DNA; this ultimately results in evolution. Organisms that share a recent ancestor have similar DNA sequences, and organisms that are more distantly related have more dissimilar DNA sequences. Hence, we can reconstruct the evolutionary history, or phylogeny, of a set of related DNA sequences by analyzing similarities in their nucleotide sequences”. – Madigan et al. 2019  Endosymbiotic mitochondria were beneficial to the early eukaryotic cells because they increased the cell’s respiratory capacity. The early mitochondria-containing cells became the ancestors of all living Eukarya. Virtually all eukaryotic cells have mitochondria, though these structures were subsequently lost in certain lineages of anaerobic microbial eukaryotes.  A second endosymbiotic event had a major impact on the evolution of life. Chloroplasts arose from the incorporation of a cyanobacterium-like cell into the cytoplasm of a eukaryotic lineage, and this endosymbiotic event triggered the origin of photosynthesis within Eukarya, the 3rd Domain of life  All phototrophic eukaryotes, including plants and algae, have descended from the lineage of cells that acquired endosymbiotic chloroplasts. Atmospheric oxygen is intimately associated with the endosymbiotic origins of organelles, being consumed by the ancestor of the mitochondrion and being produced by the ancestor of the chloroplast.  These endosymbiotic events diversified the metabolism of early eukaryotic cells, with mitochondria providing aerobic respiration and chloroplasts providing the ability to exploit sunlight for energy. The endosymbiotic origin of organelles set the stage for the diversification of Eukarya into the forms we know today. need to know these “big five” mass extinction events during the Paleozoic Era:  Ordovician period (488-444 MYA)  Devonian period (416-359 MYA)  Permian period ended with the 3rd mass extinction event (251 MYA)  Triassic period (ended with the 4th MEE, 00MYA)  Cretaceous period (ended with the 5th MEE, 65 MYA) Eukaryotic models for the origin of eukaryotes Cenozoic Era (65MYA to present) The Neogene has been marked by many ice ages, the rise of humans, and mass extinctions; most of these mass extinctions may have been caused by the ice age climate, humans, or both; the current mass extinction event (we are in one now, the sixth extinction) is mostly caused by humans Challenge questions: (a) The serial endosymbiosis hypothesis proposes that the eukaryotic ancestor diverged from the archaeal line and possessed a nucleus and other features of eukaryotic cells prior to endosymbiosis with the bacterial ancestor of the mitochondrion. A later endosymbiosis with the cyanobacterial ancestor of the chloroplast gave rise to the eukaryotic ancestor of all plants and all other photosynthetic eukaryotes. (b) The hydrogen hypothesis proposes that the eukaryotic cell evolved from a symbiotic relationship between H2-producing cells of Bacteria and H2-consuming cells of Archaea. The bacterial partner was eventually engulfed by its archaeal partner and evolved over time into the mitochondrion. The nucleus and other features of the eukaryotic cell evolved after establishment of endosymbiosis. A later endosymbiosis with the cyanobacterial ancestor of the chloroplast gave rise to the eukaryotic ancestor of all plants and all other photosynthetic eukaryotes. History of life on Earth (organized by divisions of geological time) Basis for the divisions of geologic time (see Figure on slide 27) 1. major changes in types of organisms found in the fossil record (each division has its own characteristic set of commonly found fossils and unique fossil forms) 2. many of the transitions between the divisions are marked by major extinction events, where many organisms apparently died out over a short period of time because they disappear form the fossil record from that point on 3. although there are many major extinction events in the fossil record, by most measures five stand out above the rest; you 1. What lines of reasoning support the hypothesis that the first self-replicating systems were based on RNA molecules? Answer in not more than 100 words (place word count in parentheses) 2. Why is the origin of cyanobacteria considered a critical step in evolution? Explain your answer in less than 100 words (put your word count in parentheses). 3. What kinds of evidences support the three-domain concept of life? Answer in not more than 100 words (place word count in parentheses) 4. In what ways has microbial metabolism altered Earth’s biosphere? How might life on Earth be different if oxygenic photosynthesis had not evolved? Answer in not more than 100 words (place word count in parentheses)